Run an agarose gel to determine if the DNA is degraded. Look for a tight band of high molecular weight; smearing indicates degraded DNA.

Agarose gel stained with ethidium bromide showing heat degradation of genomic DNA. This gel shows progressive degradation with increasing time of two human genomic DNA samples subjected to heating at 99°C for 0 to 30 minutes.

As the average size of the DNA in a degraded sample approaches the size of the target sequence, the amount of PCR product generated is reduced. This is due to the reduced number of intact templates in the size range necessary for amplification. An example of degradation by heating is illustrated below. Genomic DNA degraded by other causes will also deliver poor assay results.